The study of the gut microbiota has taken great interest. With advances in technology of sequencing and computer analysis, it has opened great opportunities to study bacteria like never before. The presences of gut microbes have been associated with different aspects of development and behavior. With out a doubt, the intestinal microbiota is influencing more then just nutrition. In this work we focus our study in the role that the gut bacteria could be having on sleep and the function of the immune systems in this interaction. We aimed to answer the following questions: Is the gut microbiota affected by sleep behavior? Does the gut microbiota affect sleep behavior or patterns? Is the role of macrophage activity important in sleep behavior? To answer these questions we worked with Drosophila melanogaster, an important genetic tool for which the innate immune system and sleep behavior is well understood. We used next-generation sequencing of the 16s rRNA gene to identify the composition of the gut flora during the day and night as well as flies that have been sleep deprived compared to non-deprived. We also looked at the bacteria composition of flies that are not able to compensate for lost sleep (Pumilio knock out by RNAi). In these experiments we noticed a tendency to have a decrees in bacterial sequence reads during the night as well as in sleep deprived but not in flies that cannot compensate for sleep lost. We also notice a tendency of change in abundance certain bacteria groups such as Alteromonadaceae family. To focus on the effect of the gut microbes on sleep we treated flies with a broad-spectrum antibiotic cocktail during different developmental stages. Interestingly, flies treated with antibiotic during development show a decrease in total sleep while flies treated as adult show an increase in total sleep behavior. To elucidate if macrophage activity could be having an important role in sleep regulation given that they are able to produce somnogenic substances as well as show more activity during the night, we used mutant flies that have impaired phagocytic activity to see the effect on sleep. We noticed that these flies show similar sleep structure as those flies that have been treated with antibiotics all during development, which show a decrease in total sleep. Taken together, the results seen in this work suggest that gut microbes, the immune system and sleep circuits interact to regulate sleep behavior under normal conditions, aside from that seen during an immune response against an infection. In addition, macrophage night activity seems to be playing a role in sleep regulation.